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snakemake/5.9.1 requires GCCcore-7.3.0
dvctools/1.4 requires GCCcore-5.4.0
If dvctools is loaded 2nd, then module, for some reason, downgrades GCCcore, and snakemake fails.
If dvctools is loaded 1st, then it seems to work well with GCCcore-7.3.0, and life is good.
[last: 0s][~]$ module load snakemake/5.9.1-foss-2018b-Python-3.6.6 [last: 1s][~]$ module list Currently Loaded Modules: 1) shared 9) numactl/2.0.11-GCCcore-7.3.0 17) bzip2/1.0.6-GCCcore-7.3.0 25) Python/3.6.6-foss-2018b 2) slurm/18.08.9 10) hwloc/1.11.10-GCCcore-7.3.0 18) ncurses/6.1-GCCcore-7.3.0 26) libyaml/0.2.1-GCCcore-7.3.0 3) rc-base 11) OpenMPI/3.1.1-GCC-7.3.0-2.30 19) libreadline/7.0-GCCcore-7.3.0 27) PyYAML/3.13-foss-2018b-Python-3.6.6 4) DefaultModules 12) OpenBLAS/0.3.1-GCC-7.3.0-2.30 20) Tcl/8.6.8-GCCcore-7.3.0 28) GitPython/2.1.11-foss-2018b-Python-3.6.6 5) GCCcore/7.3.0 13) gompi/2018b 21) SQLite/3.24.0-GCCcore-7.3.0 29) snakemake/5.9.1-foss-2018b-Python-3.6.6 6) binutils/2.30-GCCcore-7.3.0 14) FFTW/3.3.8-gompi-2018b 22) XZ/5.2.4-GCCcore-7.3.0 7) GCC/7.3.0-2.30 15) ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1 23) GMP/6.1.2-GCCcore-7.3.0 8) zlib/1.2.11-GCCcore-7.3.0 16) foss/2018b 24) libffi/3.2.1-GCCcore-7.3.0 [last: 0s][~]$ module load dvctools The following have been reloaded with a version change: 1) GCC/7.3.0-2.30 => GCC/5.4.0-2.26 2) GCCcore/7.3.0 => GCCcore/5.4.0 3) binutils/2.30-GCCcore-7.3.0 => binutils/2.26-GCCcore-5.4.0 [last: 1s][~]$ cd scratch/zajac/rna.sm524-2/ [last: 0s][~/scratch/zajac/rna.sm524-2]$ snakemake -n ImportError in line 1 of /scratch/curtish/zajac/rna.sm524-2/Snakefile: Missing required dependencies ['numpy'] File "/scratch/curtish/zajac/rna.sm524-2/Snakefile", line 1, in <module> File "/share/apps/rc/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/pandas-0.23.4-py3.6-linux-x86_64.egg/pandas/__init__.py", line 19, in <module> [last: 1s][~/scratch/zajac/rna.sm524-2]$
The text was updated successfully, but these errors were encountered:
Issue #5, #6: carry over fixes to most recent version of snakemake
7ee73ad
Also start loading dvctools first, to avoid GCC conflicts caused when it's loaded 2nd.
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snakemake/5.9.1 requires GCCcore-7.3.0
dvctools/1.4 requires GCCcore-5.4.0
If dvctools is loaded 2nd, then module, for some reason, downgrades GCCcore, and snakemake fails.
If dvctools is loaded 1st, then it seems to work well with GCCcore-7.3.0, and life is good.
The text was updated successfully, but these errors were encountered: